[gmx-users] K+ ions instead of NA+ for neutralization

[Justin Lemkul]

On 9/13/15 3:50 AM, Johnny Lu wrote:
> Hi. I'm new to simulation and haven't tried that. Below is what I heard.
>
> Most of the time, the force field just treat K+ and Na+ as a sphere with
> charge and with no orbitals.
> So, K+ and Na+ ions in simulations are only different in radius (of the
> sphere).
>
> I guess it is ok to use K+ instead of Na+.
>
> What forcefield did you use?
>

What are you trying to simulate?  The practical implications of the difference 
between Na+ and K+ with additive force fields are probably minimal, if 
distinguishable at all.  See, for instance, a couple of examples with DNA:

http://dx.doi.org/10.1021/jz5024543
http://dx.doi.org/10.1021/acs.jpcb.5b00683
http://dx.doi.org/10.1021/acs.jctc.5b00508

-Justin

> On Sun, Sep 13, 2015 at 3:10 AM, Andrew Bostick <andrew.bostick1 at gmail.com>
> wrote:
>
>> Dear gromacs users,
>>
>> For neutralizing the simulation system, can I use K+ ions instead of NA+?
>>
>> Best,
>> Andrew
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================